In many sequencing methods, particularly re-sequencing methods (i.e., methods in which a locus is re-sequenced), a target is first captured and then sequenced. Several target capture methodologies have been developed and integrated with high throughput sequencing systems. Specifically, hybridization-based assays using beads or microarrays and in-solution based techniques using molecular inversion probes or genomic circularization oligonucleotides can be applied to capture target DNA. Captured DNA is then prepared for sequencing. Complicated molecular biology protocols are often employed to prepare the enriched DNA sample and in certain cases production of the sequencing library involves many enzymatic reactions, purification steps and size selection by gel electrophoresis. The sample preparation process for target capture DNA sequencing can be labor intensive and subsequent sample manipulations can cause bias in the DNA content and increase the sequencing error rate.